SAXSdb — 9mli

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	9mli
沉积日期 deposition_date	2024-12-19
结构标题 title	Xenorhabdus nematophilus XptA2 RBD C Chimera
关键词 keywords	TcA, Pore Forming Toxin, TOXIN; TOXIN
实验方法 method	ELECTRON MICROSCOPY

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2. SAXS 参数 (CRYSOL 理论计算) 2. SAXS Parameters (CRYSOL)

回转半径 Rg (Guinier) rg_guinier	77.85 Å
回转半径 Rg (电子) rg_electron	77.81 Å
零角强度 I(0) i0	27612200000.00
分子量 molecular_weight	1410100.0 kDa
排除体积 excluded_volume	1760900 Å³
包络体积 envelope_volume	2756700 Å³
水化壳体积 shell_volume	284420 Å³
包络直径 envelope_diameter	262.4 Å
壳层 Rg shell_rg	87.87 Å
包络 Rg envelope_rg	75.35 Å
形状 Rg shape_rg	77.82 Å
总 Rg total_rg	77.90 Å
总原子数 total_atoms	99395
残基数 n_residues	12595
球谐函数阶数 n_harmonics	20
q 范围 q_range	— – 0.5000 Å⁻¹
数据点数 n_points	101
壳层类型 shell_type	directional
溶剂电子密度 solvent_density	0.3340 e/Å³
壳层衬度 contrast_shell	0.0300 e/Å³
CRYSOL 版本 crysol_version	4.1.3

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3. P(r) 距离分布 (GNOM 反演) 3. P(r) Analysis (GNOM)

最大尺寸 Dmax dmax	219.7 Å
Rg (实空间) rg_real	75.45 Å
Rg 误差 (实空间) rg_real_error	0.60 Å
I(0) (实空间) i0_real	2.6440e+10
I(0) 误差 (实空间) i0_real_error	5.1740e+08
Rg (倒空间) rg_reciprocal	78.10 Å
I(0) (倒空间) i0_reciprocal	27630000000.0000
解质量估计 total_estimate	0.9163
解质量评级 solution_quality	EXCELLENT a EXCELLENT solution
P(r) 峰数 n_peaks	2
主峰位置 r_peak_primary	98.8 Å
偏度 Skewness skewness	0.291
峰度 Kurtosis kurtosis	-0.213
角度范围 angular_range	— – 0.1000 Å⁻¹
当前正则化参数 α current_alpha	1.0270
最高正则化参数 α highest_alpha	18580000000.0000
实空间数据点数 n_real_points	21
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.948; Stabil: 0.965; Sysdev: 1.000; Positv: 1.000; Valcen: 0.929; Smooth: 0.243

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4. 晶体学与实验 4. Crystallography & Experiment

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5. 实体与聚合体信息 (1)

Entity 1 polymer

描述 description	A component of insecticidal toxin complex (Tc)
分子量 formula_weight	285458.3 kDa
来源方法 src_method	man
拷贝数 entity_count	5

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B,C,D,E
原子数 atom_count	99395

MYSTAVLLNKISPTRDGQTMTLADLQYLSFSELRKIFDDQLSWGEARHLYHETIEQKKNNRLLEARIFTRANPQLSGAIRLGIERDSVSRSYDEMFGARSSSFVKPGSVASMFSPAGYLTELYREAKDLHFSSSAYHLDNRRPDLADLTLSQSNMDTEISTLTLSNELLLEHITRKTGGDSDALMESLSTYRQAIDTPYHQPYETIRQVIMTHDSTLSALSRNPEVMGQAEGASLLAILANISPELYNILTEEITEKNADALFAQNFSENITPENFASQSWIAKYYGLELSEVQKYLGMLQNGYSDSTSAYVDNISTGLVVNNESKLEAYKITRVKTDDYDKNINYFDLMYEGNNQFFIRANFKVSREFGATLRKNAGPSGIVGSLSGPLIANTNFKSNYLSNISDSEYKNGVKIYAYRYTSSTSATNQGGGIFTFESYPLTIFALKLNKAIRLCLTSGLSPNELQTIVRSDNAQGIINDSVLTKVFYTLFYSHRYALSFDDAQVLNGSVINQYADDDSVSHFNRLFNTPPLKGKIFEADGNTVSIDPDEEQSTFARSALMRGLGVNSGELYQLGKLAGVLDAQNTITLSVFVISSLYRLTLLARVHQLTVNELCMLYGLSPFNGKTTASLSSGELPRLVIWLYQVTQWLTEAEITTEAIWLLCTPEFSGNISPEISNLLNNLRPSISEDMAQSHNRELQAEILAPFIAATLHLASPDMARYILLWTDNLRPGGLDIAGFMTLVLKESLNANETTQLVQFCHVMAQLSLSVQTLRLSEAELSVLVISGFAVLGAKNQPAGQHNIDTLFSLYRFHQWINGLGNPGSDTLDMLRQQTLTADRLASVMGLDISMVTQAMVSAGVNQLQCWQDINTVLQWIDVASALHTMPSVIRTLVNIRYVTALNKAESNLPSWDEWQTLAENMEAGLSTQQAQTLADYTAERLSSVLCNWFLANIQPEGVSLHSRDDLYSYFLIDNQVSSAIKTTRLAEAIAGIQLYINRALNRIEPNARADVSTRQFFTDWTVNNRYSTWGGVSRLVYYPENYIDPTQRIGQTRMMDELLENISQSKLSRDTVEDAFKTYLTRFETVADLKVVSAYHDNVNSNTGLTWFVGQTRENLPEYYWRNVDISRMQAGELAANAWKEWTKIDTAVNPYKDAIRPVIFRERLHLIWVEKEEVAKNGTDPVETYDRFTLKLAFLRHDGSWSAPWSYDITTQVEAVTDKKPDTERLALAASGFQGEDTLLVFVYKTGKSYSDFGGSNKNVAGMTIYGDGSFKKMENTALSRYSQLKNTFDIIHTQGNDLVRKASYRFAQDFEVPASLNMGSAIGDDSLTVMENGNIPQITSKYSSDNLAITLHNAAFTVRYDGSGNVIRNKQISAMKLTGVDGKSQYGNAFIIANTVKHYGGYSDLGGPITVYNKTKNYIASVQGHLMNADYTRRLILTPVENNYYARLFEFPFSPNTILNTVFTVGSNKTSDFKKCSYAVDGNNSQGFQIFSSYQSSGWLDIDTGINNTDIKITVMAGSKTHTFTASDHIASLPANSFDAMPYTFKPLEIDASSLAFTNNIAPLDIVFETKAKDGRVLGKIKQTLSVKRVNYNPEDILFLRETHSGAQYMQLGVYRIRLNTLLASQLVSRANTGIDTILTMETQRLPEPPLGEGFYATFVIPPYNLSTHGDERWFKLYIKHVVDNNSHIIYSGQLTDTNINITLFIPLDDVPLNQDYHAKVYMTFKKSPSDGTWWGPHFVRDDKGIVTINPKSILTHFESVNVLNNYSAPMDFNSASALYYWELFYYTPMMCFQRLLQEKQFDEATQWINYVYNPAGYIVNGEIAPWIWNCRPLEETTSWNANPLDAIDPDAVAQNDPMHYKIATFMRLLDQLILRGDMAYRELTRDALNEAKMWYVRTLELLGDEPEDYGSQQWAAPSLSGAASQTVQAAYQQDLTMLGRGGVSKNLRTANSLVGLFLPEYNPALTDYWQTLRLRLFNLRHNLSIDGQPLSLAIYAEPTDPKALLTSMVQASQGGSAVLPGTLSLYRFPVMLERTRNLVAQLTQFGTSLLSMAEHDDADELTTLLLQQGMELATQSIRIQQRTVDEVDADIAVLAESRRSAQNRLEKYQQLYDEDINHGEQRAMSLLDAAAGQSLAGQVLSIAEGVADLVPNVFGLACGGSRWGAALRASASVMSLSATASQYSADKISRSEAYRRRRQEWEIQRDNADGEVKQMDAQLESLKIRREAAQMQVEYQETQQAHTQAQLELLQRKFTNKALYSWMRGKLSAIYYQFFDLTQSFCLMAQEALRRELTDNGVTFIRGGAWNGTTAGLMAGETLLLNLAEMEKVWLERDERALEVTRTVSLAQFYQALSSDNFNLTEKLTQFLREGKGNVGASGNELKLSNRQIEASVRLSDLKIFSDYPESLGNTRQLKQVSVTLPALVGPYEDIRAVLNYGGSIVMPRGCSAIALSHGVNDSGQFMLDFNDSRYLPFEGISVNDSGSLTLSFPDATDRQKALLESLSDIILHIRYTIRSENLYFQGDYKDDDDKLEHHHHHH

来源 Source

来源生物 organism	Xenorhabdus nematophila
NCBI 分类编号 ncbi_taxonomy_id	628
宿主生物 host_organism	Escherichia coli

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7. 引用文献 (1)

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晶胞边长 a length_a	1.000 Å
晶胞边长 b length_b	1.000 Å
晶胞边长 c length_c	1.000 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	90.00 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	—

空间群 space_group	P 1
空间群编号 int_tables_number	1
晶系 crystal_system	—

分辨率 resolution	3.400 Å
最低分辨率 resolution_low	— Å
R 因子 r_factor	—
R_work r_work	—
R_free r_free	—

分辨率 resolution	3.40 Å
分辨率测定方法 resolution_method	—
颗粒数 num_particles	77025

fit	/app/data/saxs_computation/ml/9mli/9mli.fit
pddf	/app/data/pr_computation/ml/9mli/9mli.pr.out
profile	/app/data/saxs_computation/ml/9mli/9mli.dat

Xenorhabdus nematophilus XptA2 RBD C Chimera

SAXS 散射曲线 SAXS Profile

P(r) 距离分布 P(r) Distribution

1. 结构基本信息 1. Structure Basics

2. SAXS 参数 (CRYSOL 理论计算) 2. SAXS Parameters (CRYSOL)

3. P(r) 距离分布 (GNOM 反演) 3. P(r) Analysis (GNOM)

4. 晶体学与实验 4. Crystallography & Experiment

晶胞参数 Unit Cell

对称性 Symmetry

精修参数 Refinement

冷冻电镜 EM 3D

5. 实体与聚合体信息 (1)

Entity 1 polymer

聚合体 Polymer

来源 Source

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)